[gmx-users] Re: equilibrium stage runs for too long

[Justin Lemkul]

On 8/23/12 2:37 PM, Clare wrote:
> Hi Justin,
>
> Thank you so much for your reply!
> what could be the fundamental things that went wrong? for example, is it the
> problem of the parameters I used in my mdp file or the problem in the system
> itself?

Either, both, or neither.  Slow run times are generally incorrect .mdp 
parameters (which you haven't shown), incorrect use of mdrun (you haven't shown 
your command), or some problem external to Gromacs (MPI/threading environment, 
hardware, etc).

> The way I built my system is that, firstly I created three boxes containing
> water, lipid and decane respectively using random insertion, and I performed
> EM,NVT and NPT on each box. After this, I built a new box and placed the
> three boxes in it one by one, and finally EM was performed on this big box.
> The result from EM was:
> Steepest Descents converged to Fmax < 1000 in 168 steps
> Potential Energy  = -4.7134688e+05
> Maximum force     =  8.5041827e+02 on atom 634
> Norm of force     =  4.4439018e+01
>
> Does that show any clue?
>

None of that indicates anything that would give rise to the problem at hand. 
Your EM appears entirely normal.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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